Description Usage Arguments Details Value See Also Examples
View source: R/runEpiSDReport.R
Function to render the markdown report of alarms in HTML format for ECDC Signal Detection Report
1 | runEpiSDReport(input, stratified, outputfile)
|
input |
list of parameters as defined in the Signal Detection Application (see (i.e. (see also default parameters in
|
stratified |
a logical value indicating whether the report
should be stratified by |
outputfile |
output file name (e.g. (default value is a temporary folder - |
Datasets to use in the report:
Default dataset included in the package
(Salmonellosis 2007-2016 or Measles 1999-2018 data) (i.e. input$file = NULL
);
External dataset:
–> An export (csv format) from the ECDC Surveillance Atlas of Infectious Diseases: http://atlas.ecdc.europa.eu/public/index.aspx.
On the ECDC "Surveillance Atlas of Infectious Diseases" web site:
1- Choose the disease/health topic to analyse
2- Export the data (csv) using the default settings
3- Specify the location of this external dataset in the input
argument of the runEpiSDReport() function
(e.g. input <- list(file = list(datapath = "C:/Users/Downloads/ECDC_surveillance_data_Pertussis.csv"),
disease = "Pertussis", country = "Greece", indicator = "Reported cases",
stratification = "All cases", unit = "Month", daterange = c("2011-12-01", "2016-12-01"),
algo = "FarringtonFlexible", testingperiod = 3))
4- You can now render the re markdown report...
(e.g. runEpiSDReport(input = input)
)
–> Any dataset specified as described in the package vignette.
An HTML report
Default dataset used in the report SignalData
Signal Detection Application runEpiSDApp
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 | #-- Running the report as a standalone function
runEpiSDReport() #Definition of each input parameter
#is done one by one through the R console
#---> OR
#-- First setting the parameters to run the report for
input <- list(
disease = "Salmonellosis",
country = "Portugal",
indicator = "Reported cases",
stratification = "Confirmed cases",
unit = "Month",
daterange = c("2011-01-01", "2016-12-31"),
algo = "FarringtonFlexible",
testingperiod = 6
)
#-- Second running the report based on the EpiSignalDetection::SignalData dataset
#-- and store it in a temporary folder
runEpiSDReport(input = input)
#-- Running the report based on the EpiSignalDetection::SignalData dataset
#-- and store the HTML output 'test.html' in the folder 'C:/R/'
runEpiSDReport(input = input, outputfile = "C:/R/test.html")
#-- Running the report based on external data
input <- list(
file = list(datapath = "C:/Users/Downloads/ECDC_surveillance_data_Pertussis.csv"),
disease = "Pertussis",
country = "Greece",
indicator = "Reported cases",
stratification = "All cases",
unit = "Month",
daterange = c("2011-12-01", "2016-12-01"),
algo = "FarringtonFlexible",
testingperiod = 3
)
runEpiSDReport(input = input, stratified = TRUE)
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